A fairly nice local muni in Lakewood, Co. called Fox Hollow has three fairly distinct nines, although really only one, called the Canyon nine, has topography that is truly different. One is the inevitable "Links style" with the other called the Meadow nine (all designed by Dennis Griffith). As they are billed separately, I'm not really bothered by the differences and take it as an opportunity to get a couple of different types of vistas during the course of one round. (Rounds being all too rare right now, as I have kids aged 8, 7, 5, and four !)
What's more bothersome to me are cases like another local muni called Hyland Hills, where an existing 18 was supplemented by an added nine. A new "gold" course was established which included nine new and nine old holes. The style of play, the bunkering, greens........the differences made a round there a lot less pleasant. As long as the entire course is built at one time, though, a little digression seems acceptable..........